i agree, there are serveral reason for them to perform well other than beeing overtuned.
They work very well for engageing on carries and have overall good mechanics vs them like the massive as slow from malph or the inbuilt thornmail from rammus, in nautis case they offer massive peeling for the own carrie, but most of all they are really save.
If you have a tank like that top, you can be pretty sure that he won't feed, and he will be somewhat effective even if behind in farm. This prettymuch removes toplane as a risiko factor, allowing your jungler to focus purely on bot/mid, and if your carry gets a lead you have as good as won, same with a snowballing assasins.
They also offer rather strong tp ganks to help getting your carrie ahead, and if you have a damage focused jungler like nida or lee, a champ like naut can give them free kills vs more squishy laners post 6.
So righ offer alot benefits, they suplement the usually rather damage focused low cc teamcomps, they are save, they have strong synergie with agressive junglers, and they either have great peeling or engage, or both.
That beeing said, i do think naut is a bit overtuned. He offers relible engage, catchpotential, peeling, solid damage, waveclear, good early trades and good tankiness(as far as tankiness goes, which still means a 5+ item adc kills him in a matter of seconds)
i think they should shift some damage from his E back to the W, which would help his jungle clear whil it hits the waveclear and harras/short trades in lane and his reliable aoe damage in teamfights, while keeping good potential damage if he's alowed to AA duering W.
also with the rather stupid metagolem rising, they have an easy life in lane. Really, outside of fiora i haven't seen that built ever working out on usually squishy champ, and fiora also works well with a lifesteal focused built or other bruiser builts...
just saw a 'juggernaut-akali' face rammus top some time ago...she run out of energie and ultsteps befor anyone even was at 50%...